The death of Toshikatsu Matsuoka, who was found hanged, would be a blow to Prime Minister Shinzo Abe who had supported him against those calling for his resignation over the scandal, the Kyodo news agency reported.
Six suicide notes were found on a desk in the minister's room, Kyodo said.
Abe was quoted as telling reporters, "As he was a competent minister of agriculture, forestry and fisheries, the effects on the administration will be significant."
The prime minister declined to comment on what might have led to Matsuoka's death, saying, "It is not appropriate to make presumptions lightly.''
Chief Cabinet Secretary Yasuhisa Shiozaki said Environment Minister Masatoshi Wakabayashi has taken over Matsuoka's job on an interim basis, the report said.
Matsuoka, who became minister last September when Abe assumed office, had come under pressure over expenditures incurred in running his office.